# ##################################################################################################
#  Disclaimer                                                                                      #
#  This file is a python3 translation of AutoDockTools (v.1.5.7)                                   #
#  Modifications made by Valdes-Tresanco MS (https://github.com/Valdes-Tresanco-MS)                #
#  Tested by Valdes-Tresanco-MS and Valdes-Tresanco ME                                             #
#  There is no guarantee that it works like the original distribution,                             #
#  but feel free to tell us if you get any difference to correct the code.                         #
#                                                                                                  #
#  Please use this cite the original reference.                                                    #
#  If you think my work helps you, just keep this note intact on your program.                     #
#                                                                                                  #
#  Modification date: 4/7/20 5:48                                                                  #
#                                                                                                  #
# ##################################################################################################

# this file was generated from
#   /thr/gamow/amber7/dat/parm94.dat
#
# file format is described at:
#   http://www.amber.ucsf.edu/amber/formats.html#parm.dat
#

title = "PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs"

# this dictionary uses the Amber atom types as keys and provides
# masses and a type description as keys
atomTypes = {
    'BR': [79.900, "bromine"],
    'C ': [12.010, "sp2 C carbonyl group "],
    'CA': [12.010, "sp2 C pure aromatic (benzene)"],
    'CB': [12.010, "sp2 aromatic C, 5&6 membered ring junction"],
    'CC': [12.010, "sp2 aromatic C, 5 memb. ring HIS"],
    'CK': [12.010, "sp2 C 5 memb.ring in purines"],
    'CM': [12.010, "sp2 C  pyrimidines in pos. 5 & 6"],
    'CN': [12.010, "sp2 C aromatic 5&6 memb.ring junct.(TRP)"],
    'CQ': [12.010, "sp2 C in 5 mem.ring of purines between 2 N"],
    'CR': [12.010, "sp2 arom as CQ but in HIS"],
    'CT': [12.010, "sp3 aliphatic C"],
    'CV': [12.010, "sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)"],
    'CW': [12.010, "sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)"],
    'C*': [12.010, "sp2 arom. 5 memb.ring w/1 subst. (TRP)"],
    'C0': [40.080, "calcium"],
    'F ': [19.000, "fluorine"],
    'H ': [1.008, "H bonded to nitrogen atoms"],
    'HC': [1.008, "H aliph. bond. to C without electrwd.group"],
    'H1': [1.008, "H aliph. bond. to C with 1 electrwd. group"],
    'H2': [1.008, "H aliph. bond. to C with 2 electrwd.groups"],
    'H3': [1.008, "H aliph. bond. to C with 3 eletrwd.groups"],
    'HA': [1.008, "H arom. bond. to C without elctrwd. groups"],
    'H4': [1.008, "H arom. bond. to C with 1 electrwd. group"],
    'H5': [1.008, "H arom. bond. to C with 2 electrwd. groups"],
    'HO': [1.008, "hydroxyl group"],
    'HS': [1.008, "hydrogen bonded to sulphur"],
    'HW': [1.008, "H in TIP3P water"],
    'HP': [1.008, "H bonded to C next to positively charged gr"],
    'I ': [126.900, "iodine"],
    'IM': [35.450, "assumed to be Cl-"],
    'IP': [22.990, "assumed to be Na+"],
    'IB': [131.000, "'big ion w/ waters' for vacuum (Na+, 6H2O)"],
    'MG': [24.305, "magnesium"],
    'N ': [14.010, "sp2 nitrogen in amide groups"],
    'NA': [14.010, "sp2 N in 5 memb.ring w/H atom (HIS)"],
    'NB': [14.010, "sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)"],
    'NC': [14.010, "sp2 N in 6 memb.ring w/LP (ADE,GUA)"],
    'N2': [14.010, "sp2 N in amino groups"],
    'N3': [14.010, "sp3 N for charged amino groups (Lys, etc)"],
    'N*': [14.010, "sp2 N "],
    'O ': [16.000, "carbonyl group oxygen"],
    'OW': [16.000, "oxygen in TIP3P water"],
    'OH': [16.000, "oxygen in hydroxyl group"],
    'OS': [16.000, "ether and ester oxygen"],
    'O2': [16.000, "carboxyl and phosphate group oxygen"],
    'P ': [30.970, "phosphate"],
    'S ': [32.060, "sulphur in disulfide linkage"],
    'SH': [32.060, "sulphur in cystine"],
    'CU': [63.550, "copper"],
    'FE': [55.000, "iron"],
    'Li': [6.940, "lithium"],
    'K ': [39.100, "potassium"],
    'Rb': [85.470, "rubidium"],
    'Cs': [132.910, "cesium"]
}

# The atom symbols which are hydrophilic in solution.
# This information is read but not used.
JSOLTY = ['C', 'H', 'HO', 'N', 'NA', 'NB', 'NC', 'N2', 'NT', 'N2', 'N3',
          'N*', 'O', 'OH', 'OS', 'P', 'O2 ']

# INPUT FOR BOND LENGTH PARAMETERS
# IBT,JBT    Atom symbols for the two bonded atoms.
#         RK         The harmonic force constant for the bond "IBT"-"JBT".
#                    The unit is kcal/mol/(A**2).
#
#         REQ        The equilibrium bond length for the above bond in 
#                    angstroms. The input is terminated by a blank card.


bondTypes = {
    'OW-HW': [553.0, 0.9572, "TIP3P water"],
    'HW-HW': [553.0, 1.5136, "TIP3P water"],
    'C -CA': [469.0, 1.409, "JCC,7,(1986),230; TYR"],
    'C -CB': [447.0, 1.419, "JCC,7,(1986),230; GUA"],
    'C -CM': [410.0, 1.444, "JCC,7,(1986),230; THY,URA"],
    'C -CT': [317.0, 1.522, "JCC,7,(1986),230; AA"],
    'C -N*': [424.0, 1.383, "JCC,7,(1986),230; CYT,URA"],
    'C -NA': [418.0, 1.388, "JCC,7,(1986),230; GUA.URA"],
    'C -NC': [457.0, 1.358, "JCC,7,(1986),230; CYT"],
    'C -O ': [570.0, 1.229, "JCC,7,(1986),230; AA,CYT,GUA,THY,URA"],
    'C -O2': [656.0, 1.250, "JCC,7,(1986),230; GLU,ASP"],
    'C -OH': [450.0, 1.364, "JCC,7,(1986),230; TYR"],
    'CA-CA': [469.0, 1.400, "JCC,7,(1986),230; BENZENE,PHE,TRP,TYR"],
    'CA-CB': [469.0, 1.404, "JCC,7,(1986),230; ADE,TRP"],
    'CA-CM': [427.0, 1.433, "JCC,7,(1986),230; CYT"],
    'CA-CT': [317.0, 1.510, "JCC,7,(1986),230; PHE,TYR"],
    'CA-HA': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR"],
    'CA-H4': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; no assigned"],
    'CA-N2': [481.0, 1.340, "JCC,7,(1986),230; ARG,CYT,GUA"],
    'CA-NA': [427.0, 1.381, "JCC,7,(1986),230; GUA"],
    'CA-NC': [483.0, 1.339, "JCC,7,(1986),230; ADE,CYT,GUA"],
    'CB-CB': [520.0, 1.370, "JCC,7,(1986),230; ADE,GUA"],
    'CB-N*': [436.0, 1.374, "JCC,7,(1986),230; ADE,GUA"],
    'CB-NB': [414.0, 1.391, "JCC,7,(1986),230; ADE,GUA"],
    'CB-NC': [461.0, 1.354, "JCC,7,(1986),230; ADE,GUA"],
    'CK-H5': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; ADE,GUA"],
    'CK-N*': [440.0, 1.371, "JCC,7,(1986),230; ADE,GUA"],
    'CK-NB': [529.0, 1.304, "JCC,7,(1986),230; ADE,GUA"],
    'CM-CM': [549.0, 1.350, "JCC,7,(1986),230; CYT,THY,URA"],
    'CM-CT': [317.0, 1.510, "JCC,7,(1986),230; THY"],
    'CM-HA': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; CYT,URA"],
    'CM-H4': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; CYT,URA"],
    'CM-H5': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; not assigned"],
    'CM-N*': [448.0, 1.365, "JCC,7,(1986),230; CYT,THY,URA"],
    'CQ-H5': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; ADE"],
    'CQ-NC': [502.0, 1.324, "JCC,7,(1986),230; ADE"],
    'CT-CT': [310.0, 1.526, "JCC,7,(1986),230; AA, SUGARS"],
    'CT-HC': [340.0, 1.090, "changed from 331 bsd on NMA nmodes; AA, SUGARS"],
    'CT-H1': [340.0, 1.090, "changed from 331 bsd on NMA nmodes; AA, RIBOSE"],
    'CT-H2': [340.0, 1.090, "changed from 331 bsd on NMA nmodes; SUGARS"],
    'CT-H3': [340.0, 1.090, "changed from 331 bsd on NMA nmodes; not assigned"],
    'CT-HP': [340.0, 1.090, " changed from 331; AA-lysine, methyl ammonium cation"],
    'CT-N*': [337.0, 1.475, "JCC,7,(1986),230; ADE,CYT,GUA,THY,URA"],
    'CT-N2': [337.0, 1.463, "JCC,7,(1986),230; ARG"],
    'CT-OH': [320.0, 1.410, "JCC,7,(1986),230; SUGARS"],
    'CT-OS': [320.0, 1.410, "JCC,7,(1986),230; NUCLEIC ACIDS"],
    'H -N2': [434.0, 1.010, "JCC,7,(1986),230; ADE,CYT,GUA,ARG"],
    'H -N*': [434.0, 1.010, "for plain unmethylated bases ADE,CYT,GUA,ARG"],
    'H -NA': [434.0, 1.010, "JCC,7,(1986),230; GUA,URA,HIS"],
    'HO-OH': [553.0, 0.960, "JCC,7,(1986),230; SUGARS,SER,TYR"],
    'HO-OS': [553.0, 0.960, "JCC,7,(1986),230; NUCLEOTIDE ENDS"],
    'O2-P ': [525.0, 1.480, "JCC,7,(1986),230; NA PHOSPHATES"],
    'OH-P ': [230.0, 1.610, "JCC,7,(1986),230; NA PHOSPHATES"],
    'OS-P ': [230.0, 1.610, "JCC,7,(1986),230; NA PHOSPHATES"],
    'C*-HC': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes, not needed AA"],
    'C -N ': [490.0, 1.335, "JCC,7,(1986),230; AA"],
    'C*-CB': [388.0, 1.459, "JCC,7,(1986),230; TRP"],
    'C*-CT': [317.0, 1.495, "JCC,7,(1986),230; TRP"],
    'C*-CW': [546.0, 1.352, "JCC,7,(1986),230; TRP"],
    'CA-CN': [469.0, 1.400, "JCC,7,(1986),230; TRP"],
    'CB-CN': [447.0, 1.419, "JCC,7,(1986),230; TRP"],
    'CC-CT': [317.0, 1.504, "JCC,7,(1986),230; HIS"],
    'CC-CV': [512.0, 1.375, "JCC,7,(1986),230; HIS(delta)"],
    'CC-CW': [518.0, 1.371, "JCC,7,(1986),230; HIS(epsilon)"],
    'CC-NA': [422.0, 1.385, "JCC,7,(1986),230; HIS"],
    'CC-NB': [410.0, 1.394, "JCC,7,(1986),230; HIS"],
    'CN-NA': [428.0, 1.380, "JCC,7,(1986),230; TRP"],
    'CR-H5': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes;HIS"],
    'CR-NA': [477.0, 1.343, "JCC,7,(1986),230; HIS"],
    'CR-NB': [488.0, 1.335, "JCC,7,(1986),230; HIS"],
    'CT-N ': [337.0, 1.449, "JCC,7,(1986),230; AA"],
    'CT-N3': [367.0, 1.471, "JCC,7,(1986),230; LYS"],
    'CT-S ': [227.0, 1.810, "changed from 222.0 based on dimethylS nmodes"],
    'CT-SH': [237.0, 1.810, "changed from 222.0 based on methanethiol nmodes"],
    'CV-H4': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes; HIS"],
    'CV-NB': [410.0, 1.394, "JCC,7,(1986),230; HIS"],
    'CW-H4': [367.0, 1.080, "changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)"],
    'CW-NA': [427.0, 1.381, "JCC,7,(1986),230; HIS,TRP"],
    'H -N ': [434.0, 1.010, "JCC,7,(1986),230; AA"],
    'H -N3': [434.0, 1.010, "JCC,7,(1986),230; LYS    "],
    'HS-SH': [274.0, 1.336, "JCC,7,(1986),230; CYS"],
    'S -S ': [166.0, 2.038, "JCC,7,(1986),230; CYX   (SCHERAGA)"],
    'CT-F ': [367.0, 1.380, "JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3"]
}

##       ***** INPUT FOR BOND ANGLE PARAMETERS *****
##               ITT , JTT , KTT , TK , TEQ
##    ITT,...    The atom symbols for the atoms making an angle.
##    TK         The harmonic force constants for the angle "ITT"-"JTT"-
##               "KTT" in units of kcal/mol/(rad**2) (radians are the
##               traditional unit for angle parameters in force fields).
##    TEQ        The equilibrium bond angle for the above angle in degrees.

bondAngles = {
    'HW-OW-HW': [100., 104.52, "TIP3P water"],
    'HW-HW-OW': [0., 127.74, "(found in crystallographic water with 3 bonds)"],
    'CB-C -NA': [70.0, 111.30, "NA"],
    'CB-C -O ': [80.0, 128.80, ""],
    'CM-C -NA': [70.0, 114.10, ""],
    'CM-C -O ': [80.0, 125.30, ""],
    'CT-C -O ': [80.0, 120.40, ""],
    'CT-C -O2': [70.0, 117.00, ""],
    'CT-C -OH': [70.0, 117.00, ""],
    'N*-C -NA': [70.0, 115.40, ""],
    'N*-C -NC': [70.0, 118.60, ""],
    'N*-C -O ': [80.0, 120.90, ""],
    'NA-C -O ': [80.0, 120.60, ""],
    'NC-C -O ': [80.0, 122.50, ""],
    'CT-C -N ': [70.0, 116.60, "AA general"],
    'N -C -O ': [80.0, 122.90, "AA general"],
    'O -C -O ': [80.0, 126.00, "AA COO- terminal residues"],
    'O2-C -O2': [80.0, 126.00, "AA GLU            (SCH JPC 79,2379)"],
    'O -C -OH': [80.0, 126.00, ""],
    'CA-C -CA': [63.0, 120.00, "changed from 85.0  bsd on C6H6 nmodes; AA tyr"],
    'CA-C -OH': [70.0, 120.00, "AA tyr"],
    'C -CA-CA': [63.0, 120.00, "changed from 85.0  bsd on C6H6 nmodes"],
    'CA-CA-CA': [63.0, 120.00, "changed from 85.0  bsd on C6H6 nmodes"],
    'CA-CA-CB': [63.0, 120.00, "changed from 85.0  bsd on C6H6 nmodes"],
    'CA-CA-CT': [70.0, 120.00, ""],
    'CA-CA-HA': [35.0, 120.00, ""],
    'CA-CA-H4': [35.0, 120.00, ""],
    'CB-CA-HA': [35.0, 120.00, ""],
    'CB-CA-H4': [35.0, 120.00, ""],
    'CB-CA-N2': [70.0, 123.50, ""],
    'CB-CA-NC': [70.0, 117.30, ""],
    'CM-CA-N2': [70.0, 120.10, ""],
    'CM-CA-NC': [70.0, 121.50, ""],
    'N2-CA-NA': [70.0, 116.00, ""],
    'N2-CA-NC': [70.0, 119.30, ""],
    'NA-CA-NC': [70.0, 123.30, ""],
    'C -CA-HA': [35.0, 120.00, "AA tyr"],
    'N2-CA-N2': [70.0, 120.00, "AA arg"],
    'CN-CA-HA': [35.0, 120.00, "AA trp"],
    'CA-CA-CN': [63.0, 120.00, "changed from 85.0  bsd on C6H6 nmodes; AA trp"],
    'C -CB-CB': [63.0, 119.20, "changed from 85.0  bsd on C6H6 nmodes; NA gua"],
    'C -CB-NB': [70.0, 130.00, ""],
    'CA-CB-CB': [63.0, 117.30, "changed from 85.0  bsd on C6H6 nmodes; NA ade"],
    'CA-CB-NB': [70.0, 132.40, ""],
    'CB-CB-N*': [70.0, 106.20, ""],
    'CB-CB-NB': [70.0, 110.40, ""],
    'CB-CB-NC': [70.0, 127.70, ""],
    'N*-CB-NC': [70.0, 126.20, ""],
    'C*-CB-CA': [63.0, 134.90, "changed from 85.0  bsd on C6H6 nmodes; AA trp"],
    'C*-CB-CN': [63.0, 108.80, "changed from 85.0  bsd on C6H6 nmodes; AA trp"],
    'CA-CB-CN': [63.0, 116.20, "changed from 85.0  bsd on C6H6 nmodes; AA trp"],
    'H5-CK-N*': [35.0, 123.05, ""],
    'H5-CK-NB': [35.0, 123.05, ""],
    'N*-CK-NB': [70.0, 113.90, ""],
    'C -CM-CM': [63.0, 120.70, "changed from 85.0  bsd on C6H6 nmodes; NA thy"],
    'C -CM-CT': [70.0, 119.70, ""],
    'C -CM-HA': [35.0, 119.70, ""],
    'C -CM-H4': [35.0, 119.70, ""],
    'CA-CM-CM': [63.0, 117.00, "changed from 85.0  bsd on C6H6 nmodes; NA cyt"],
    'CA-CM-HA': [35.0, 123.30, ""],
    'CA-CM-H4': [35.0, 123.30, ""],
    'CM-CM-CT': [70.0, 119.70, ""],
    'CM-CM-HA': [35.0, 119.70, ""],
    'CM-CM-H4': [35.0, 119.70, ""],
    'CM-CM-N*': [70.0, 121.20, ""],
    'H4-CM-N*': [35.0, 119.10, ""],
    'H5-CQ-NC': [35.0, 115.45, ""],
    'NC-CQ-NC': [70.0, 129.10, ""],
    'CM-CT-HC': [50.0, 109.50, "changed based on NMA nmodes"],
    'CT-CT-CT': [40.0, 109.50, ""],
    'CT-CT-HC': [50.0, 109.50, "changed based on NMA nmodes"],
    'CT-CT-H1': [50.0, 109.50, "changed based on NMA nmodes"],
    'CT-CT-H2': [50.0, 109.50, "changed based on NMA nmodes"],
    'CT-CT-HP': [50.0, 109.50, "changed based on NMA nmodes"],
    'CT-CT-N*': [50.0, 109.50, ""],
    'CT-CT-OH': [50.0, 109.50, ""],
    'CT-CT-OS': [50.0, 109.50, ""],
    'HC-CT-HC': [35.0, 109.50, ""],
    'H1-CT-H1': [35.0, 109.50, ""],
    'HP-CT-HP': [35.0, 109.50, "AA lys, ch3nh4+"],
    'H2-CT-N*': [50.0, 109.50, "changed based on NMA nmodes"],
    'H1-CT-N*': [50.0, 109.50, "changed based on NMA nmodes"],
    'H1-CT-OH': [50.0, 109.50, "changed based on NMA nmodes "],
    'H1-CT-OS': [50.0, 109.50, "changed based on NMA nmodes "],
    'H2-CT-OS': [50.0, 109.50, "changed based on NMA nmodes"],
    'N*-CT-OS': [50.0, 109.50, ""],
    'H1-CT-N ': [50.0, 109.50, "AA general  changed based on NMA nmodes"],
    'C -CT-H1': [50.0, 109.50, "AA general  changed based on NMA nmodes"],
    'C -CT-HP': [50.0, 109.50, "AA zwitterion  changed based on NMA nmodes"],
    'H1-CT-S ': [50.0, 109.50, "AA cys     changed based on NMA nmodes"],
    'H1-CT-SH': [50.0, 109.50, "AA cyx     changed based on NMA nmodes"],
    'CT-CT-S ': [50.0, 114.70, "AA cyx            (SCHERAGA  JPC 79,1428)"],
    'CT-CT-SH': [50.0, 108.60, "AA cys"],
    'H2-CT-H2': [35.0, 109.50, "AA lys"],
    'H1-CT-N2': [50.0, 109.50, "AA arg     changed based on NMA nmodes"],
    'HP-CT-N3': [50.0, 109.50, "AA lys, ch3nh3+, changed based on NMA nmodes"],
    'CA-CT-CT': [63.0, 114.00, "AA phe tyr          (SCH JPC  79,2379)"],
    'C -CT-HC': [50.0, 109.50, "AA gln      changed based on NMA nmodes"],
    'C -CT-N ': [63.0, 110.10, "AA general"],
    'CT-CT-N2': [80.0, 111.20, "AA arg             (JCP 76, 1439)"],
    'CT-CT-N ': [80.0, 109.70, "AA ala, general    (JACS 94, 2657)"],
    'C -CT-CT': [63.0, 111.10, "AA general"],
    'CA-CT-HC': [50.0, 109.50, "AA tyr     changed based on NMA nmodes"],
    'CT-CT-N3': [80.0, 111.20, "AA lys             (JCP 76, 1439)"],
    'CC-CT-CT': [63.0, 113.10, "AA his"],
    'CC-CT-HC': [50.0, 109.50, "AA his     changed based on NMA nmodes"],
    'C -CT-N3': [80.0, 111.20, "AA amino terminal residues"],
    'C*-CT-CT': [63.0, 115.60, "AA trp"],
    'C*-CT-HC': [50.0, 109.50, "AA trp    changed based on NMA nmodes"],
    'CT-CC-NA': [70.0, 120.00, "AA his"],
    'CT-CC-CV': [70.0, 120.00, "AA his"],
    'CT-CC-NB': [70.0, 120.00, "AA his"],
    'CV-CC-NA': [70.0, 120.00, "AA his"],
    'CW-CC-NA': [70.0, 120.00, "AA his"],
    'CW-CC-NB': [70.0, 120.00, "AA his"],
    'CT-CC-CW': [70.0, 120.00, "AA his"],
    'H5-CR-NA': [35.0, 120.00, "AA his"],
    'H5-CR-NB': [35.0, 120.00, "AA his"],
    'NA-CR-NA': [70.0, 120.00, "AA his"],
    'NA-CR-NB': [70.0, 120.00, "AA his"],
    'CC-CV-H4': [35.0, 120.00, "AA his"],
    'CC-CV-NB': [70.0, 120.00, "AA his"],
    'H4-CV-NB': [35.0, 120.00, "AA his"],
    'CC-CW-H4': [35.0, 120.00, "AA his"],
    'CC-CW-NA': [70.0, 120.00, "AA his"],
    'H4-CW-NA': [35.0, 120.00, "AA his"],
    'C*-CW-H4': [35.0, 120.00, "AA trp"],
    'C*-CW-NA': [70.0, 108.70, "AA trp"],
    'CT-C*-CW': [70.0, 125.00, "AA trp"],
    'CB-C*-CT': [70.0, 128.60, "AA trp"],
    'CB-C*-CW': [63.0, 106.40, "changed from 85.0  bsd on C6H6 nmodes; AA trp"],
    'CA-CN-NA': [70.0, 132.80, "AA trp"],
    'CB-CN-NA': [70.0, 104.40, "AA trp"],
    'CA-CN-CB': [63.0, 122.70, "changed from 85.0  bsd on C6H6 nmodes; AA trp"],
    'C -N -CT': [50.0, 121.90, "AA general"],
    'C -N -H ': [30.0, 120.00, "AA general, gln, asn,changed based on NMA nmodes"],
    'CT-N -H ': [30.0, 118.04, "AA general,     changed based on NMA nmodes"],
    'CT-N -CT': [50.0, 118.00, "AA pro             (DETAR JACS 99,1232)"],
    'H -N -H ': [35.0, 120.00, "ade,cyt,gua,gln,asn     **"],
    'C -N*-CM': [70.0, 121.60, ""],
    'C -N*-CT': [70.0, 117.60, ""],
    'C -N*-H ': [30.0, 119.20, "changed based on NMA nmodes"],
    'CB-N*-CK': [70.0, 105.40, ""],
    'CB-N*-CT': [70.0, 125.80, ""],
    'CB-N*-H ': [30.0, 125.80, "for unmethylated n.a. bases,chngd bsd NMA nmodes"],
    'CK-N*-CT': [70.0, 128.80, ""],
    'CK-N*-H ': [30.0, 128.80, "for unmethylated n.a. bases,chngd bsd NMA nmodes"],
    'CM-N*-CT': [70.0, 121.20, ""],
    'CM-N*-H ': [30.0, 121.20, "for unmethylated n.a. bases,chngd bsd NMA nmodes"],
    'CA-N2-H ': [35.0, 120.00, ""],
    'H -N2-H ': [35.0, 120.00, ""],
    'CT-N2-H ': [35.0, 118.40, "AA arg"],
    'CA-N2-CT': [50.0, 123.20, "AA arg"],
    'CT-N3-H ': [50.0, 109.50, "AA lys,     changed based on NMA nmodes"],
    'CT-N3-CT': [50.0, 109.50, "AA pro/nt"],
    'H -N3-H ': [35.0, 109.50, "AA lys, AA(end)"],
    'C -NA-C ': [70.0, 126.40, ""],
    'C -NA-CA': [70.0, 125.20, ""],
    'C -NA-H ': [30.0, 116.80, "changed based on NMA nmodes"],
    'CA-NA-H ': [30.0, 118.00, "changed based on NMA nmodes"],
    'CC-NA-CR': [70.0, 120.00, "AA his"],
    'CC-NA-H ': [30.0, 120.00, "AA his,    changed based on NMA nmodes"],
    'CR-NA-CW': [70.0, 120.00, "AA his"],
    'CR-NA-H ': [30.0, 120.00, "AA his,    changed based on NMA nmodes"],
    'CW-NA-H ': [30.0, 120.00, "AA his,    changed based on NMA nmodes"],
    'CN-NA-CW': [70.0, 111.60, "AA trp"],
    'CN-NA-H ': [30.0, 123.10, "AA trp,    changed based on NMA nmodes"],
    'CB-NB-CK': [70.0, 103.80, ""],
    'CC-NB-CR': [70.0, 117.00, "AA his"],
    'CR-NB-CV': [70.0, 117.00, "AA his"],
    'C -NC-CA': [70.0, 120.50, ""],
    'CA-NC-CB': [70.0, 112.20, ""],
    'CA-NC-CQ': [70.0, 118.60, ""],
    'CB-NC-CQ': [70.0, 111.00, ""],
    'C -OH-HO': [35.0, 113.00, ""],
    'CT-OH-HO': [55.0, 108.50, ""],
    'HO-OH-P ': [45.0, 108.50, ""],
    'CT-OS-CT': [60.0, 109.50, ""],
    'CT-OS-P ': [100.0, 120.50, ""],
    'P -OS-P ': [100.0, 120.50, ""],
    'O2-P -OH': [45.0, 108.23, ""],
    'O2-P -O2': [140.0, 119.90, ""],
    'O2-P -OS': [100.0, 108.23, ""],
    'OH-P -OS': [45.0, 102.60, ""],
    'OS-P -OS': [45.0, 102.60, ""],
    'CT-S -CT': [62.0, 98.90, "AA met"],
    'CT-S -S ': [68.0, 103.70, "AA cyx             (SCHERAGA  JPC 79,1428)"],
    'CT-SH-HS': [43.0, 96.00, "changed from 44.0 based on methanethiol nmodes"],
    'HS-SH-HS': [35.0, 92.07, "AA cys"],
    'F -CT-F ': [77.0, 109.10, "JCC,13,(1992),963;"],
    'F -CT-H1': [35.0, 109.50, "JCC,13,(1992),963;"]
}

##   -      ***** INPUT FOR DIHEDRAL PARAMETERS *****
##                IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
##     IPT, ...   The atom symbols for the atoms forming a dihedral
##                angle.  If IPT .eq. 'X ' .and. LPT .eq. 'X ' then
##                any dihedrals in the system involving the atoms "JPT" and
##                and "KPT" are assigned the same parameters.  This is
##                called the general dihedral type and is of the form
##                "X "-"JPT"-"KPT"-"X ".
##
##     IDIVF      The factor by which the torsional barrier is divided.
##                Consult Weiner, et al., JACS 106:765 (1984) p. 769 for
##                details. Basically, the actual torsional potential is
##
##                       (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
##
##     PK         The barrier height divided by a factor of 2.
##
##     PHASE      The phase shift angle in the torsional function.
##
##                The unit is degrees.
##
##     PN         The periodicity of the torsional barrier.
##                NOTE: If PN .lt. 0.0 then the torsional potential
##                      is assumed to have more than one term, and the
##                      values of the rest of the terms are read from the
##                      next cards until a positive PN is encountered.  The
##                      negative value of pn is used only for identifying
##                      the existence of the next term and only the
##                      absolute value of PN is kept.

dihedTypes = {
    'X -C -CA-X ': [[4, 14.50, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -C -CB-X ': [[4, 12.00, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -C -CM-X ': [[4, 8.70, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -C -N*-X ': [[4, 5.80, 180.0, 2., "JCC,7,(1986),230"]],
    'X -C -NA-X ': [[4, 5.40, 180.0, 2., "JCC,7,(1986),230"]],
    'X -C -NC-X ': [[2, 8.00, 180.0, 2., "JCC,7,(1986),230"]],
    'X -C -OH-X ': [[2, 1.80, 180.0, 2., "JCC,7,(1986),230"]],
    'X -C -CT-X ': [[4, 0.00, 0.0, 2., "JCC,7,(1986),230"]],
    'X -CA-CA-X ': [[4, 14.50, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CA-CB-X ': [[4, 14.00, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CA-CM-X ': [[4, 10.20, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CA-CT-X ': [[6, 0.00, 0.0, 2., "JCC,7,(1986),230"]],
    'X -CA-N2-X ': [[4, 9.60, 180.0, 2., "reinterpolated 93'"]],
    'X -CA-NA-X ': [[4, 6.00, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CA-NC-X ': [[2, 9.60, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CB-CB-X ': [[4, 21.80, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CB-N*-X ': [[4, 6.60, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CB-NB-X ': [[2, 5.10, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CB-NC-X ': [[2, 8.30, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CK-N*-X ': [[4, 6.80, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CK-NB-X ': [[2, 20.00, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CM-CM-X ': [[4, 26.60, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CM-CT-X ': [[6, 0.00, 0.0, 3., "JCC,7,(1986),230"]],
    'X -CM-N*-X ': [[4, 7.40, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CQ-NC-X ': [[2, 13.60, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CT-CT-X ': [[9, 1.40, 0.0, 3., "JCC,7,(1986),230"]],
    'X -CT-N -X ': [[6, 0.00, 0.0, 2., "JCC,7,(1986),230"]],
    'X -CT-N*-X ': [[6, 0.00, 0.0, 2., "JCC,7,(1986),230"]],
    'X -CT-N2-X ': [[6, 0.00, 0.0, 3., "JCC,7,(1986),230"]],
    'X -CT-OH-X ': [[3, 0.50, 0.0, 3., "JCC,7,(1986),230"]],
    'X -CT-OS-X ': [[3, 1.15, 0.0, 3., "JCC,7,(1986),230"]],
    'X -OH-P -X ': [[3, 0.75, 0.0, 3., "JCC,7,(1986),230"]],
    'X -OS-P -X ': [[3, 0.75, 0.0, 3., "JCC,7,(1986),230"]],
    'X -C -N -X ': [[4, 10.00, 180.0, 2., "AA|check Wendy?&NMA"]],
    'X -CT-N3-X ': [[9, 1.40, 0.0, 3., "JCC,7,(1986),230"]],
    'X -CT-S -X ': [[3, 1.00, 0.0, 3., "JCC,7,(1986),230"]],
    'X -CT-SH-X ': [[3, 0.75, 0.0, 3., "JCC,7,(1986),230"]],
    'X -C*-CB-X ': [[4, 6.70, 180.0, 2., "intrpol.bsd.onC6H6aa"]],
    'X -C*-CT-X ': [[6, 0.00, 0.0, 2., "JCC,7,(1986),230"]],
    'X -C*-CW-X ': [[4, 26.10, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CA-CN-X ': [[4, 14.50, 180.0, 2., "reinterpolated 93'"]],
    'X -CB-CN-X ': [[4, 12.00, 180.0, 2., "reinterpolated 93'"]],
    'X -CC-CT-X ': [[6, 0.00, 0.0, 2., "JCC,7,(1986),230"]],
    'X -CC-CV-X ': [[4, 20.60, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CC-CW-X ': [[4, 21.50, 180.0, 2., "intrpol.bsd.on C6H6"]],
    'X -CC-NA-X ': [[4, 5.60, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CC-NB-X ': [[2, 4.80, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CN-NA-X ': [[4, 6.10, 180.0, 2., "reinterpolated 93'"]],
    'X -CR-NA-X ': [[4, 9.30, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CR-NB-X ': [[2, 10.00, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CV-NB-X ': [[2, 4.80, 180.0, 2., "JCC,7,(1986),230"]],
    'X -CW-NA-X ': [[4, 6.00, 180.0, 2., "JCC,7,(1986),230"]],
    'CT-CT-OS-CT': [[1, 0.383, 0.0, -3., ""],
                    [1, 0.1, 180.0, 2., ""]],
    'C -N -CT-C ': [[1, 0.20, 180.0, 2., ""]],
    'N -CT-C -N ': [[1, 0.40, 180.0, -4., ""],
                    [1, 1.35, 180.0, -2., ""],
                    [1, 0.75, 180.0, 1., ""]],
    'CT-CT-N -C ': [[1, 0.50, 180.0, -4., ""],
                    [1, 0.15, 180.0, -3., ""],
                    [1, 0.53, 0.0, 1., ""]],
    'CT-CT-C -N ': [[1, 0.100, 0.0, -4., ""],
                    [1, 0.07, 0.0, 2., ""]],
    'H -N -C -O ': [[1, 2.50, 180.0, -2., "JCC,7,(1986),230"],
                    [1, 2.00, 0.0, 1., "J.C.cistrans-NMA DE"]],
    'CT-S -S -CT': [[1, 3.50, 0.0, -2., "JCC,7,(1986),230"],
                    [1, 0.60, 0.0, 3., "JCC,7,(1986),230"]],
    'OS-CT-CT-OS': [[1, 0.144, 0.0, -3., "JCC,7,(1986),230"],
                    [1, 1.00, 0.0, 2., "pucker anal (93')"]],
    'OS-CT-CT-OH': [[1, 0.144, 0.0, -3., "JCC,7,(1986),230"],
                    [1, 1.00, 0.0, 2., "pucker anal (93')"]],
    'OH-CT-CT-OH': [[1, 0.144, 0.0, -3., "JCC,7,(1986),230"],
                    [1, 1.00, 0.0, 2., "check glicolWC? puc"]],
    'OH-P -OS-CT': [[1, 0.25, 0.0, -3., "JCC,7,(1986),230"],
                    [1, 1.20, 0.0, 2., "gg&gt ene.631g*/mp2"]],
    'OS-P -OS-CT': [[1, 0.25, 0.0, -3., "JCC,7,(1986),230"],
                    [1, 1.20, 0.0, 2., "gg&gt ene.631g*/mp2"]],
    'OS-CT-N*-CK': [[1, 0.50, 180.0, -2., "sugar frag calc (PC)"],
                    [1, 2.50, 0.0, 1., "sugar frag calc (PC)"]],
    'OS-CT-N*-CM': [[1, 0.50, 180.0, -2., "sugar frag calc (PC)"],
                    [1, 2.50, 0.0, 1., "sugar frag calc (PC)"]]
}

##  ***** INPUT FOR IMPROPER DIHEDRAL PARAMETERS *****
##
##      IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN
##
##      The input is the same as in for the dihedrals except that
##      the torsional barrier height is NOT divided by the factor
##      idivf.  The improper torsions are defined between any four
##      atoms not bonded (in a successive fashion) with each other
##      as in the case of "regular" or "proper" dihedrals.  Improper
##      dihedrals are used to keep certain groups planar and to
##      prevent the racemization of certain centers in the united
##      atom model.  Consult the above reference for details.
##
##      Important note: all general type improper dihedrals
##                      (e.g. x -x -ct-hc) should appear before all
##                      specifics (ct-ct-ct-hc) in the parm list.
##                      Otherwise the generals will override the
##                      specific with no warning.

improperDihed = {
    'X -X -C -O ': [10.5, 180., 2., "JCC,7,(1986),230"],
    'X -O2-C -O2': [10.5, 180., 2., "JCC,7,(1986),230"],
    'X -X -N -H ': [1.0, 180., 2., "JCC,7,(1986),230"],
    'X -X -N2-H ': [1.0, 180., 2., "JCC,7,(1986),230"],
    'X -X -NA-H ': [1.0, 180., 2., "JCC,7,(1986),230"],
    'X -N2-CA-N2': [10.5, 180., 2., "JCC,7,(1986),230"],
    'X -CT-N -CT': [1.0, 180., 2., "JCC,7,(1986),230"],
    'X -X -CA-HA': [1.1, 180., 2., "bsd.on C6H6 nmodes"],
    'X -X -CW-H4': [1.1, 180., 2., ""],
    'X -X -CR-H5': [1.1, 180., 2., ""],
    'X -X -CV-H4': [1.1, 180., 2., ""],
    'X -X -CQ-H5': [1.1, 180., 2., ""],
    'X -X -CK-H5': [1.1, 180., 2., ""],
    'X -X -CM-H4': [1.1, 180., 2., ""],
    'X -X -CM-HA': [1.1, 180., 2., ""],
    'X -X -CA-H4': [1.1, 180., 2., "bsd.on C6H6 nmodes "],
    'X -X -CA-H5': [1.1, 180., 2., "bsd.on C6H6 nmodes"],
    'CK-CB-N*-CT': [1.0, 180., 2., ""],
    'CM-C -N*-CT': [1.0, 180., 2., "dac guess, 9/94"],
    'CM-C -CM-CT': [1.1, 180., 2., ""],
    'CT-O -C -OH': [10.5, 180., 2., ""],
    'NA-CV-CC-CT': [1.1, 180., 2., ""],
    'NB-CW-CC-CT': [1.1, 180., 2., ""],
    'NA-CW-CC-CT': [1.1, 180., 2., ""],
    'CW-CB-C*-CT': [1.1, 180., 2., ""],
    'CA-CA-CA-CT': [1.1, 180., 2., ""],
    'C -CM-CM-CT': [1.1, 180., 2., "dac guess, 9/94"],
    'NC-CM-CA-N2': [1.1, 180., 2., "dac guess, 9/94"],
    'CB-NC-CA-N2': [1.1, 180., 2., "dac, 10/94"],
    'NA-NC-CA-N2': [1.1, 180., 2., "dac, 10/94"],
    'CA-CA-C -OH': [1.1, 180., 2., ""],
}

##  ***** INPUT FOR H-BOND 10-12 POTENTIAL PARAMETERS *****
##  KT1 , KT2 , A , B , ASOLN , BSOLN , HCUT , IC
##  KT1,KT2    The atom symbols for the atom pairs for which the
##             parameters are defined.
##  A          The coefficient of the 12th power term (A/(r**12)).
##  B          The coefficient of the 10th power term (-B/(r**10)).

Hbonds = ['HW', 'OW', 0., 0.]

##      ***** INPUT FOR EQUIVALENCING ATOM SYMBOLS FOR
##                     THE NON-BONDED 6-12 POTENTIAL PARAMETERS *****
##                     IORG , IEQV(I) , I = 1 , 19
##
##    IORG        The atom symbols to which other atom symbols are to be
##                equivalenced in generating the 6-12 potential parameters.
##
##    IEQV(I)     The atoms symbols which are to be equivalenced to the
##                atom symbol "IORG".  If more than 19 atom symbols have
##                to be equivalenced to a given atom symbol they can be
##                included as extra cards.
##
##                It is advisable not to equivalence any hydrogen bond
##                atom type atoms with any other atom types.

AtomEquiv = {'N': ['NA', 'N2', 'N*', 'NC', 'NB', 'N3', 'NP', 'NO'],
             'C': ['C*', 'CA', 'CB', 'CC', 'CN', 'CM', 'CK', 'CQ', 'CW',
                   'CV', 'CR', 'CA', 'CX', 'CY', 'CD'],
             'O': ['O2'],  # check this with DAC
             'H': ['HS'],  # check this with DAC
             'S': ['SH'],  # check this with DAC
             }

##       ***** INPUT FOR THE 6-12 POTENTIAL PARAMETERS *****
##               LABEL , KINDNB
##
##   LABEL       The name of the non-bonded input parameter to be
##               used.  It has to be matched with "NAMNB" read through
##               unit 5.  The program searches the file to load the
##               the required non-bonded parameters.  If that name is
##               not found the run will be terminated.
##
##   KINDNB      Flag for the type of 6-12 parameters.
##
##    'SK'       Slater-Kirkwood parameters are input.
##               see "caution" below.
##
##    'RE'       van der Waals radius and the potential well depth
##               parameters are read.
##
##    'AC'       The 6-12 potential coefficients are read.
##
##       NOTE: All the non equivalenced atoms' parameters have to
##                     be given.

potParam = {
    'H ': [0.6000, 0.0157, "Ferguson base pair geom."],
    'HO': [0.0000, 0.0000, "OPLS Jorgensen, JACS,110,(1988),1657"],
    'HS': [0.6000, 0.0157, "W. Cornell CH3SH --> CH3OH FEP"],
    'HC': [1.4870, 0.0157, "OPLS"],
    'H1': [1.3870, 0.0157, "Veenstra et al JCC,8,(1992),963 "],
    'H2': [1.2870, 0.0157, "Veenstra et al JCC,8,(1992),963 "],
    'H3': [1.1870, 0.0157, "Veenstra et al JCC,8,(1992),963 "],
    'HP': [1.1000, 0.0157, "Veenstra et al JCC,8,(1992),963"],
    'HA': [1.4590, 0.0150, "Spellmeyer "],
    'H4': [1.4090, 0.0150, "Spellmeyer, one electrowithdr. neighbor"],
    'H5': [1.3590, 0.0150, "Spellmeyer, two electrowithdr. neighbor"],
    'HW': [0.0000, 0.0000, "TIP3P water model"],
    'O ': [1.6612, 0.2100, "OPLS"],
    'O2': [1.6612, 0.2100, "OPLS"],
    'OW': [1.7683, 0.1520, "TIP3P water model"],
    'OH': [1.7210, 0.2104, "OPLS "],
    'OS': [1.6837, 0.1700, "OPLS ether"],
    'CT': [1.9080, 0.1094, "Spellmeyer"],
    'CA': [1.9080, 0.0860, "Spellmeyer"],
    'CM': [1.9080, 0.0860, "Spellmeyer"],
    'C ': [1.9080, 0.0860, "OPLS"],
    'N ': [1.8240, 0.1700, "OPLS"],
    'S ': [2.0000, 0.2500, "W. Cornell CH3SH and CH3SCH3 FEP's"],
    'SH': [2.0000, 0.2500, "W. Cornell CH3SH and CH3SCH3 FEP's"],
    'P ': [2.1000, 0.2000, "JCC,7,(1986),230; "],
    'IM': [2.47, 0.1, "Cl- Smith & Dang, JCP 1994,100:5,3757"],
    'Li': [1.1370, 0.0183, "Li+ Aqvist JPC 1990,94,8021. (adapted)"],
    'IP': [1.8680, 0.00277, "Na+ Aqvist JPC 1990,94,8021. (adapted)"],
    'K ': [2.6580, 0.000328, "K+  Aqvist JPC 1990,94,8021. (adapted)"],
    'Rb': [2.9560, 0.00017, "Rb+ Aqvist JPC 1990,94,8021. (adapted)"],
    'Cs': [3.3950, 0.0000806, "Cs+ Aqvist JPC 1990,94,8021. (adapted)"],
    'I ': [2.35, 0.40, "JCC,7,(1986),230;  "],
    'F ': [1.75, 0.061, "Gough et al. JCC 13,(1992),963."],
    'IB': [5.0, 0.1, "solvated ion for vacuum approximation"],
}
